9cg3

Human kidney respiratory complex III

Method: ELECTRON MICROSCOPY Dmax: 176.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome b-c1 complex subunit 8

OrganismNot specified

UniProt O14949

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain A; UniProt 1–82 Chain N; UniProt 1–82 Not recorded Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR8_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–82; UniProt 1–82 Author chain N; PDBConstruct 1–82; UniProt 1–82

Cytochrome b-c1 complex subunit Rieske, mitochondrial

OrganismNot specified

UniProt P47985

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain C; UniProt 1–274 Chain P; UniProt 1–274 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UCRI_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–274; UniProt 1–274 Author chain P; PDBConstruct 1–274; UniProt 1–274

Cytochrome b-c1 complex subunit 9

OrganismNot specified

UniProt Q9UDW1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain D; UniProt 1–63 Chain Q; UniProt 1–63 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR9_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–63; UniProt 1–63 Author chain Q; PDBConstruct 1–63; UniProt 1–63

Cytochrome b-c1 complex subunit 6, mitochondrial

OrganismNot specified

UniProt P07919

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain E; UniProt 1–91 Chain R; UniProt 1–91 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR6_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–91; UniProt 1–91 Author chain R; PDBConstruct 1–91; UniProt 1–91

Cytochrome b-c1 complex subunit 7

OrganismNot specified

UniProt P14927

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain F; UniProt 1–111 Chain S; UniProt 1–111 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR7_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain F; PDBConstruct 1–111; UniProt 1–111 Author chain S; PDBConstruct 1–111; UniProt 1–111

Cytochrome b-c1 complex subunit 10

OrganismNot specified

UniProt O14957

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain G; UniProt 1–56 Chain T; UniProt 1–56 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR10_HUMAN
Isoform
PDB entities 6
Chains and sequence ranges Author chain G; PDBConstruct 1–56; UniProt 1–56 Author chain T; PDBConstruct 1–56; UniProt 1–56

Cytochrome c1, heme protein, mitochondrial

OrganismNot specified

UniProt P08574

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain H; UniProt 1–325 Chain U; UniProt 1–325 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CY1_HUMAN
Isoform
PDB entities 7
Chains and sequence ranges Author chain H; PDBConstruct 1–325; UniProt 1–325 Author chain U; PDBConstruct 1–325; UniProt 1–325

Cytochrome b

OrganismNot specified

UniProt P00156

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain J; UniProt 1–380 Chain V; UniProt 1–380 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYB_HUMAN
Isoform
PDB entities 8
Chains and sequence ranges Author chain J; PDBConstruct 1–380; UniProt 1–380 Author chain V; PDBConstruct 1–380; UniProt 1–380

Cytochrome b-c1 complex subunit 2, mitochondrial

OrganismNot specified

UniProt P22695

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain K; UniProt 1–453 Chain W; UniProt 1–453 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 1, mitochondrial × 2 (P31930) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR2_HUMAN
Isoform
PDB entities 9
Chains and sequence ranges Author chain K; PDBConstruct 1–453; UniProt 1–453 Author chain W; PDBConstruct 1–453; UniProt 1–453

Cytochrome b-c1 complex subunit 1, mitochondrial

OrganismNot specified

UniProt P31930

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 20 PDB declaration: 20-meric(20) Consistent with protein copy count Chain L; UniProt 1–480 Chain Y; UniProt 1–480 Not recorded Cytochrome b-c1 complex subunit 8 × 2 (O14949) Cytochrome b-c1 complex subunit Rieske, mitochondrial × 2 (P47985) Cytochrome b-c1 complex subunit 9 × 2 (Q9UDW1) Cytochrome b-c1 complex subunit 6, mitochondrial × 2 (P07919) Cytochrome b-c1 complex subunit 7 × 2 (P14927) Cytochrome b-c1 complex subunit 10 × 2 (O14957) Cytochrome c1, heme protein, mitochondrial × 2 (P08574) Cytochrome b × 2 (P00156) Cytochrome b-c1 complex subunit 2, mitochondrial × 2 (P22695) FES FE2/S2 (INORGANIC) CLUSTER × 2 HEC HEME C × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name QCR1_HUMAN
Isoform
PDB entities 10
Chains and sequence ranges Author chain L; PDBConstruct 1–480; UniProt 1–480 Author chain Y; PDBConstruct 1–480; UniProt 1–480

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9cg3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cg3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cg3
Deposition date deposition_date2024-06-28
Structure title titleHuman kidney respiratory complex III
Keywords keywordshuman, kidney, respiratory complex III, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.75
Radius of gyration Rg (electron density) rg_electron53.83
Forward intensity I(0) i02778630000.00
Molecular weight molecular_weight451770.0 kDa
Excluded volume excluded_volume568900 ų
Envelope volume envelope_volume812200 ų
Hydration-shell volume shell_volume122910 ų
Envelope diameter envelope_diameter172.5
Shell Rg shell_rg59.19
Envelope Rg envelope_rg52.36
Shape Rg shape_rg53.82
Total Rg total_rg54.01
Total atoms total_atoms31844
Residues n_residues3994
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax176.6
Rg (real space) rg_real54.60
Rg uncertainty (real space) rg_real_error1.25
I(0) (real space) i0_real2.7790e+09
I(0) uncertainty (real space) i0_real_error4.9530e+07
Rg (reciprocal space) rg_reciprocal54.86
I(0) (reciprocal space) i0_reciprocal2780000000.0000
Solution quality estimate total_estimate0.8852
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary67.0
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.553
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha277800000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.794

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (13)

8. Citations (1)

9. Files and Curves (10)